Is the floor level? How is the flange roughed in? Cast iron, plastic, copper?? If the flange is that far off, you might want to correct the situation which means taking the flange off and installing it level.

: The toilet closet flange in my roughed-in basement bathroom is not level with the concrete floor (approx 1 5/8" on one side of the 7" flange and 2 1/8" on the other side). I have yet to install the sub floor. Does this have to be levelled or will the wax ring compensate for that much uneveness? If it must be levelled, how can it be done? Thank you.